| 1 |
/* |
| 2 |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
* |
| 4 |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
* redistribute this software in source and binary code form, provided |
| 7 |
* that the following conditions are met: |
| 8 |
* |
| 9 |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
* notice, this list of conditions and the following disclaimer. |
| 11 |
* |
| 12 |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
* notice, this list of conditions and the following disclaimer in the |
| 14 |
* documentation and/or other materials provided with the |
| 15 |
* distribution. |
| 16 |
* |
| 17 |
* This software is provided "AS IS," without a warranty of any |
| 18 |
* kind. All express or implied conditions, representations and |
| 19 |
* warranties, including any implied warranty of merchantability, |
| 20 |
* fitness for a particular purpose or non-infringement, are hereby |
| 21 |
* excluded. The University of Notre Dame and its licensors shall not |
| 22 |
* be liable for any damages suffered by licensee as a result of |
| 23 |
* using, modifying or distributing the software or its |
| 24 |
* derivatives. In no event will the University of Notre Dame or its |
| 25 |
* licensors be liable for any lost revenue, profit or data, or for |
| 26 |
* direct, indirect, special, consequential, incidental or punitive |
| 27 |
* damages, however caused and regardless of the theory of liability, |
| 28 |
* arising out of the use of or inability to use software, even if the |
| 29 |
* University of Notre Dame has been advised of the possibility of |
| 30 |
* such damages. |
| 31 |
* |
| 32 |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
* research, please cite the appropriate papers when you publish your |
| 34 |
* work. Good starting points are: |
| 35 |
* |
| 36 |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
*/ |
| 42 |
|
| 43 |
/** |
| 44 |
* @file Molecule.hpp |
| 45 |
* @author tlin |
| 46 |
* @date 10/25/2004 |
| 47 |
* @version 1.0 |
| 48 |
*/ |
| 49 |
|
| 50 |
#ifndef PRIMITIVES_MOLECULE_HPP |
| 51 |
#define PRIMITIVES_MOLECULE_HPP |
| 52 |
#include <vector> |
| 53 |
#include <iostream> |
| 54 |
|
| 55 |
#include "constraints/ConstraintPair.hpp" |
| 56 |
#include "math/Vector3.hpp" |
| 57 |
#include "primitives/Atom.hpp" |
| 58 |
#include "primitives/RigidBody.hpp" |
| 59 |
#include "primitives/Bond.hpp" |
| 60 |
#include "primitives/Bend.hpp" |
| 61 |
#include "primitives/Torsion.hpp" |
| 62 |
#include "primitives/Inversion.hpp" |
| 63 |
#include "primitives/CutoffGroup.hpp" |
| 64 |
#include "utils/PropertyMap.hpp" |
| 65 |
|
| 66 |
namespace OpenMD{ |
| 67 |
|
| 68 |
class Constraint; |
| 69 |
|
| 70 |
/** |
| 71 |
* @class Molecule Molecule.hpp "primitives/Molecule.hpp" |
| 72 |
* @brief |
| 73 |
*/ |
| 74 |
class Molecule { |
| 75 |
public: |
| 76 |
|
| 77 |
typedef std::vector<Atom*>::iterator AtomIterator; |
| 78 |
typedef std::vector<Bond*>::iterator BondIterator; |
| 79 |
typedef std::vector<Bend*>::iterator BendIterator; |
| 80 |
typedef std::vector<Torsion*>::iterator TorsionIterator; |
| 81 |
typedef std::vector<Inversion*>::iterator InversionIterator; |
| 82 |
typedef std::vector<RigidBody*>::iterator RigidBodyIterator; |
| 83 |
typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator; |
| 84 |
typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator; |
| 85 |
typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator; |
| 86 |
typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator; |
| 87 |
typedef std::vector<Atom*>::iterator FluctuatingChargeIterator; |
| 88 |
|
| 89 |
Molecule(int stampId, int globalIndex, const std::string& molName); |
| 90 |
virtual ~Molecule(); |
| 91 |
|
| 92 |
/** |
| 93 |
* Returns the global index of this molecule. |
| 94 |
* @return the global index of this molecule |
| 95 |
*/ |
| 96 |
int getGlobalIndex() { |
| 97 |
return globalIndex_; |
| 98 |
} |
| 99 |
|
| 100 |
/** |
| 101 |
* Returns the stamp id of this molecule |
| 102 |
* @note Ideally, every molecule should keep a pointer of its |
| 103 |
* molecule stamp instead of its stamp id. However, the pointer |
| 104 |
* will become invalid, if the molecule migrate to other |
| 105 |
* processor. |
| 106 |
*/ |
| 107 |
int getStampId() { |
| 108 |
return stampId_; |
| 109 |
} |
| 110 |
|
| 111 |
/** Returns the name of the molecule */ |
| 112 |
std::string getType() { |
| 113 |
return moleculeName_; |
| 114 |
} |
| 115 |
|
| 116 |
/** |
| 117 |
* Sets the global index of this molecule. |
| 118 |
* @param new global index to be set |
| 119 |
*/ |
| 120 |
void setGlobalIndex(int index) { |
| 121 |
globalIndex_ = index; |
| 122 |
} |
| 123 |
|
| 124 |
void setConstrainedCharge(RealType cc) { |
| 125 |
constrainedCharge_ = cc; |
| 126 |
} |
| 127 |
|
| 128 |
RealType getConstrainedCharge() { |
| 129 |
return constrainedCharge_; |
| 130 |
} |
| 131 |
|
| 132 |
/** add an atom into this molecule */ |
| 133 |
void addAtom(Atom* atom); |
| 134 |
|
| 135 |
/** add a bond into this molecule */ |
| 136 |
void addBond(Bond* bond); |
| 137 |
|
| 138 |
/** add a bend into this molecule */ |
| 139 |
void addBend(Bend* bend); |
| 140 |
|
| 141 |
/** add a torsion into this molecule*/ |
| 142 |
void addTorsion(Torsion* torsion); |
| 143 |
|
| 144 |
/** add an improper torsion into this molecule*/ |
| 145 |
void addInversion(Inversion* inversion); |
| 146 |
|
| 147 |
/** add a rigidbody into this molecule */ |
| 148 |
void addRigidBody(RigidBody *rb); |
| 149 |
|
| 150 |
/** add a cutoff group into this molecule */ |
| 151 |
void addCutoffGroup(CutoffGroup* cp); |
| 152 |
|
| 153 |
void addConstraintPair(ConstraintPair* consPair); |
| 154 |
|
| 155 |
void addConstraintElem(ConstraintElem* consElem); |
| 156 |
|
| 157 |
/** */ |
| 158 |
void complete(); |
| 159 |
|
| 160 |
/** Returns the total number of atoms in this molecule */ |
| 161 |
unsigned int getNAtoms() { |
| 162 |
return atoms_.size(); |
| 163 |
} |
| 164 |
|
| 165 |
/** Returns the total number of bonds in this molecule */ |
| 166 |
unsigned int getNBonds(){ |
| 167 |
return bonds_.size(); |
| 168 |
} |
| 169 |
|
| 170 |
/** Returns the total number of bends in this molecule */ |
| 171 |
unsigned int getNBends() { |
| 172 |
return bends_.size(); |
| 173 |
} |
| 174 |
|
| 175 |
/** Returns the total number of torsions in this molecule */ |
| 176 |
unsigned int getNTorsions() { |
| 177 |
return torsions_.size(); |
| 178 |
} |
| 179 |
|
| 180 |
/** Returns the total number of improper torsions in this molecule */ |
| 181 |
unsigned int getNInversions() { |
| 182 |
return inversions_.size(); |
| 183 |
} |
| 184 |
|
| 185 |
/** Returns the total number of rigid bodies in this molecule */ |
| 186 |
unsigned int getNRigidBodies() { |
| 187 |
return rigidBodies_.size(); |
| 188 |
} |
| 189 |
|
| 190 |
/** Returns the total number of integrable objects in this molecule */ |
| 191 |
unsigned int getNIntegrableObjects() { |
| 192 |
return integrableObjects_.size(); |
| 193 |
} |
| 194 |
|
| 195 |
/** Returns the total number of cutoff groups in this molecule */ |
| 196 |
unsigned int getNCutoffGroups() { |
| 197 |
return cutoffGroups_.size(); |
| 198 |
} |
| 199 |
|
| 200 |
/** Returns the total number of constraints in this molecule */ |
| 201 |
unsigned int getNConstraintPairs() { |
| 202 |
return constraintPairs_.size(); |
| 203 |
} |
| 204 |
|
| 205 |
/** Returns the total number of fluctuating charges in this molecule */ |
| 206 |
unsigned int getNFluctuatingCharges() { |
| 207 |
return fluctuatingCharges_.size(); |
| 208 |
} |
| 209 |
|
| 210 |
Atom* getAtomAt(unsigned int i) { |
| 211 |
assert(i < atoms_.size()); |
| 212 |
return atoms_[i]; |
| 213 |
} |
| 214 |
|
| 215 |
RigidBody* getRigidBodyAt(unsigned int i) { |
| 216 |
assert(i < rigidBodies_.size()); |
| 217 |
return rigidBodies_[i]; |
| 218 |
} |
| 219 |
|
| 220 |
Atom* beginAtom(std::vector<Atom*>::iterator& i) { |
| 221 |
i = atoms_.begin(); |
| 222 |
return (i == atoms_.end()) ? NULL : *i; |
| 223 |
} |
| 224 |
|
| 225 |
Atom* nextAtom(std::vector<Atom*>::iterator& i) { |
| 226 |
++i; |
| 227 |
return (i == atoms_.end()) ? NULL : *i; |
| 228 |
} |
| 229 |
|
| 230 |
Bond* beginBond(std::vector<Bond*>::iterator& i) { |
| 231 |
i = bonds_.begin(); |
| 232 |
return (i == bonds_.end()) ? NULL : *i; |
| 233 |
} |
| 234 |
|
| 235 |
Bond* nextBond(std::vector<Bond*>::iterator& i) { |
| 236 |
++i; |
| 237 |
return (i == bonds_.end()) ? NULL : *i; |
| 238 |
|
| 239 |
} |
| 240 |
|
| 241 |
Bend* beginBend(std::vector<Bend*>::iterator& i) { |
| 242 |
i = bends_.begin(); |
| 243 |
return (i == bends_.end()) ? NULL : *i; |
| 244 |
} |
| 245 |
|
| 246 |
Bend* nextBend(std::vector<Bend*>::iterator& i) { |
| 247 |
++i; |
| 248 |
return (i == bends_.end()) ? NULL : *i; |
| 249 |
} |
| 250 |
|
| 251 |
Torsion* beginTorsion(std::vector<Torsion*>::iterator& i) { |
| 252 |
i = torsions_.begin(); |
| 253 |
return (i == torsions_.end()) ? NULL : *i; |
| 254 |
} |
| 255 |
|
| 256 |
Torsion* nextTorsion(std::vector<Torsion*>::iterator& i) { |
| 257 |
++i; |
| 258 |
return (i == torsions_.end()) ? NULL : *i; |
| 259 |
} |
| 260 |
|
| 261 |
Inversion* beginInversion(std::vector<Inversion*>::iterator& i) { |
| 262 |
i = inversions_.begin(); |
| 263 |
return (i == inversions_.end()) ? NULL : *i; |
| 264 |
} |
| 265 |
|
| 266 |
Inversion* nextInversion(std::vector<Inversion*>::iterator& i) { |
| 267 |
++i; |
| 268 |
return (i == inversions_.end()) ? NULL : *i; |
| 269 |
} |
| 270 |
|
| 271 |
RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i) { |
| 272 |
i = rigidBodies_.begin(); |
| 273 |
return (i == rigidBodies_.end()) ? NULL : *i; |
| 274 |
} |
| 275 |
|
| 276 |
RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i) { |
| 277 |
++i; |
| 278 |
return (i == rigidBodies_.end()) ? NULL : *i; |
| 279 |
} |
| 280 |
|
| 281 |
StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) { |
| 282 |
i = integrableObjects_.begin(); |
| 283 |
return (i == integrableObjects_.end()) ? NULL : *i; |
| 284 |
} |
| 285 |
|
| 286 |
StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) { |
| 287 |
++i; |
| 288 |
return (i == integrableObjects_.end()) ? NULL : *i; |
| 289 |
} |
| 290 |
|
| 291 |
CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) { |
| 292 |
i = cutoffGroups_.begin(); |
| 293 |
return (i == cutoffGroups_.end()) ? NULL : *i; |
| 294 |
} |
| 295 |
|
| 296 |
CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) { |
| 297 |
++i; |
| 298 |
return (i == cutoffGroups_.end()) ? NULL : *i; |
| 299 |
} |
| 300 |
|
| 301 |
ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) { |
| 302 |
i = constraintPairs_.begin(); |
| 303 |
return (i == constraintPairs_.end()) ? NULL : *i; |
| 304 |
} |
| 305 |
|
| 306 |
ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) { |
| 307 |
++i; |
| 308 |
return (i == constraintPairs_.end()) ? NULL : *i; |
| 309 |
} |
| 310 |
|
| 311 |
ConstraintElem* beginConstraintElem(std::vector<ConstraintElem*>::iterator& i) { |
| 312 |
i = constraintElems_.begin(); |
| 313 |
return (i == constraintElems_.end()) ? NULL : *i; |
| 314 |
} |
| 315 |
|
| 316 |
ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) { |
| 317 |
++i; |
| 318 |
return (i == constraintElems_.end()) ? NULL : *i; |
| 319 |
} |
| 320 |
|
| 321 |
Atom* beginFluctuatingCharge(std::vector<Atom*>::iterator& i) { |
| 322 |
i = fluctuatingCharges_.begin(); |
| 323 |
return (i == fluctuatingCharges_.end()) ? NULL : *i; |
| 324 |
} |
| 325 |
|
| 326 |
Atom* nextFluctuatingCharge(std::vector<Atom*>::iterator& i) { |
| 327 |
++i; |
| 328 |
return (i == fluctuatingCharges_.end()) ? NULL : *i; |
| 329 |
} |
| 330 |
|
| 331 |
|
| 332 |
/** |
| 333 |
* Returns the total potential energy of short range interaction |
| 334 |
* of this molecule |
| 335 |
*/ |
| 336 |
RealType getPotential(); |
| 337 |
|
| 338 |
/** get total mass of this molecule */ |
| 339 |
RealType getMass(); |
| 340 |
|
| 341 |
/** return the center of mass of this molecule */ |
| 342 |
Vector3d getCom(); |
| 343 |
|
| 344 |
/** Moves the center of this molecule */ |
| 345 |
void moveCom(const Vector3d& delta); |
| 346 |
|
| 347 |
/** Returns the velocity of center of mass of this molecule */ |
| 348 |
Vector3d getComVel(); |
| 349 |
|
| 350 |
std::string getMoleculeName() { |
| 351 |
return moleculeName_; |
| 352 |
} |
| 353 |
|
| 354 |
friend std::ostream& operator <<(std::ostream& o, Molecule& mol); |
| 355 |
|
| 356 |
//below functions are just forward functions |
| 357 |
/** |
| 358 |
* Adds property into property map |
| 359 |
* @param genData GenericData to be added into PropertyMap |
| 360 |
*/ |
| 361 |
void addProperty(GenericData* genData); |
| 362 |
|
| 363 |
/** |
| 364 |
* Removes property from PropertyMap by name |
| 365 |
* @param propName the name of property to be removed |
| 366 |
*/ |
| 367 |
void removeProperty(const std::string& propName); |
| 368 |
|
| 369 |
/** |
| 370 |
* clear all of the properties |
| 371 |
*/ |
| 372 |
void clearProperties(); |
| 373 |
|
| 374 |
/** |
| 375 |
* Returns all names of properties |
| 376 |
* @return all names of properties |
| 377 |
*/ |
| 378 |
std::vector<std::string> getPropertyNames(); |
| 379 |
|
| 380 |
/** |
| 381 |
* Returns all of the properties in PropertyMap |
| 382 |
* @return all of the properties in PropertyMap |
| 383 |
*/ |
| 384 |
std::vector<GenericData*> getProperties(); |
| 385 |
|
| 386 |
/** |
| 387 |
* Returns property |
| 388 |
* @param propName name of property |
| 389 |
* @return a pointer point to property with propName. If no property named propName |
| 390 |
* exists, return NULL |
| 391 |
*/ |
| 392 |
GenericData* getPropertyByName(const std::string& propName); |
| 393 |
|
| 394 |
private: |
| 395 |
|
| 396 |
int globalIndex_; |
| 397 |
|
| 398 |
std::vector<Atom*> atoms_; |
| 399 |
std::vector<Bond*> bonds_; |
| 400 |
std::vector<Bend*> bends_; |
| 401 |
std::vector<Torsion*> torsions_; |
| 402 |
std::vector<Inversion*> inversions_; |
| 403 |
std::vector<RigidBody*> rigidBodies_; |
| 404 |
std::vector<StuntDouble*> integrableObjects_; |
| 405 |
std::vector<CutoffGroup*> cutoffGroups_; |
| 406 |
std::vector<ConstraintPair*> constraintPairs_; |
| 407 |
std::vector<ConstraintElem*> constraintElems_; |
| 408 |
std::vector<Atom*> fluctuatingCharges_; |
| 409 |
int stampId_; |
| 410 |
std::string moleculeName_; |
| 411 |
PropertyMap properties_; |
| 412 |
RealType constrainedCharge_; |
| 413 |
|
| 414 |
}; |
| 415 |
|
| 416 |
} //namespace OpenMD |
| 417 |
#endif // |
